Many JavaScript libraries (especially non-recent ones) do not handle IE9 well because it breaks with IE8 in the handling of a lot of things.
JS code that sniffs for IE will fail quite frequently in IE9, unless such code is rewritten to handle IE9 specifically.
Before the JS code is updated, you should use the "X-UA-Compatible" meta tag to force your web page into IE8 mode.
EDIT: Can't believe that, 3 years later and we're onto IE11, and there are still up-votes for this. :-) Many JS libraries should now at least support IE9 natively and most support IE10, so it is unlikely that you'll need the meta tag these days, unless you don't intend to upgrade your JS library. But beware that IE10 changes things regarding to cross-domain scripting and some CDN-based library code breaks. Check your library version. For example, Dojo 1.9 on the CDN will break on IE10, but 1.9.1 solves it.
EDIT 2: You REALLY need to get your acts together now. We are now in mid-2014!!! I am STILL getting up-votes for this! Revise your sites to get rid of old-IE hard-coded dependencies!
Sigh... If I had known that this would be by far my most popular answer, I'd probably have spent more time polishing it...
EDIT 3: It is now almost 2016. Upvotes still ticking up... I guess there are lots of legacy code out there... One day our programs will out-live us...
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